On 22/03/2012 5:13 AM, francesco oteri wrote:
Hi Mark,
these are the involved residues extracted by the .top (CSA and CSB are
cysteines with modified partial charges):
; residue 62 CSB rtp CSB q -0.5
1010 NH1 62 CSB N 1010 -0.47 14.007
; qtot 0.53
1011 H 62 CSB HN 1011 0.31 1.008
; qtot 0.84
1012 CT1 62 CSB CA 1012 0.07 12.011
; qtot 0.91
1013 HB 62 CSB HA 1013 0.09 1.008
; qtot 1
1014 CT2 62 CSB CB 1014 -0.05 12.011
; qtot 0.95
1015 HA 62 CSB HB1 1015 0.051 1.008
; qtot 1.001
1016 HA 62 CSB HB2 1016 0.051 1.008
; qtot 1.052
1017 S 62 CSB SG 1017 -0.57 32.06
; qtot 0.482
1018 C 62 CSB C 1018 0.51 12.011
; qtot 0.992
1019 O 62 CSB O 1019 -0.51 15.999
; qtot 0.482
; residue 65 CSA rtp CSA q -0.3
1043 NH1 65 CSA N 1043 -0.47 14.007
; qtot 0.012
1044 H 65 CSA HN 1044 0.31 1.008
; qtot 0.322
1045 CT1 65 CSA CA 1045 0.07 12.011
; qtot 0.392
1046 HB 65 CSA HA 1046 0.09 1.008
; qtot 0.482
1047 CT2 65 CSA CB 1047 -0.03 12.011
; qtot 0.452
1048 HA 65 CSA HB1 1048 0.08 1.008
; qtot 0.532
1049 HA 65 CSA HB2 1049 0.08 1.008
; qtot 0.612
1050 S 65 CSA SG 1050 -0.39 32.06
; qtot 0.222
1051 C 65 CSA C 1051 0.51 12.011
; qtot 0.732
1052 O 65 CSA O 1052 -0.51 15.999
; qtot 0.222
; residue 112 ASN rtp ASN q 0.0
1006 NH1 112 ASN N 1006 -0.47 14.007
; qtot -4.732
1007 H 112 ASN HN 1007 0.31 1.008
; qtot -4.422
1008 CT1 112 ASN CA 1008 0.07 12.011
; qtot -4.352
1009 HB 112 ASN HA 1009 0.09 1.008
; qtot -4.262
1010 CT2 112 ASN CB 1010 -0.18 12.011
; qtot -4.442
1011 HA 112 ASN HB1 1011 0.09 1.008
; qtot -4.352
1012 HA 112 ASN HB2 1012 0.09 1.008
; qtot -4.262
1013 CC 112 ASN CG 1013 0.55 12.011
; qtot -3.712
1014 O 112 ASN OD1 1014 -0.55 15.999
; qtot -4.262
1015 NH2 112 ASN ND2 1015 -0.62 14.007
; qtot -4.882
1016 H 112 ASN HD21 1016 0.32 1.008
; qtot -4.562
1017 H 112 ASN HD22 1017 0.3 1.008
; qtot -4.262
1018 C 112 ASN C 1018 0.51 12.011
; qtot -3.752
1019 O 112 ASN O 1019 -0.51 15.999
; qtot -4.262
; residue 114 ILE rtp ILE q 0.0
1041 NH1 114 ILE N 1041 -0.47 14.007
; qtot -4.732
1042 H 114 ILE HN 1042 0.31 1.008
; qtot -4.422
1043 CT1 114 ILE CA 1043 0.07 12.011
; qtot -4.352
1044 HB 114 ILE HA 1044 0.09 1.008
; qtot -4.262
1045 CT1 114 ILE CB 1045 -0.09 12.011
; qtot -4.352
1046 HA 114 ILE HB 1046 0.09 1.008
; qtot -4.262
1047 CT3 114 ILE CG2 1047 -0.27 12.011
; qtot -4.532
1048 HA 114 ILE HG21 1048 0.09 1.008
; qtot -4.442
1049 HA 114 ILE HG22 1049 0.09 1.008
; qtot -4.352
1050 HA 114 ILE HG23 1050 0.09 1.008
; qtot -4.262
1051 CT2 114 ILE CG1 1051 -0.18 12.011
; qtot -4.442
1052 HA 114 ILE HG11 1052 0.09 1.008
; qtot -4.352
1053 HA 114 ILE HG12 1053 0.09 1.008
; qtot -4.262
1054 CT3 114 ILE CD 1054 -0.27 12.011
; qtot -4.532
1055 HA 114 ILE HD1 1055 0.09 1.008
; qtot -4.442
1056 HA 114 ILE HD2 1056 0.09 1.008
; qtot -4.352
1057 HA 114 ILE HD3 1057 0.09 1.008
; qtot -4.262
1058 C 114 ILE C 1058 0.51 12.011
; qtot -3.752
1059 O 114 ILE O 1059 -0.51 15.999
; qtot -4.262
; residue 607 CSB rtp CSB q -0.5
9693 NH1 607 CSB N 9693 -0.47 14.007
; qtot -3.248
9694 H 607 CSB HN 9694 0.31 1.008
; qtot -2.938
9695 CT1 607 CSB CA 9695 0.07 12.011
; qtot -2.868
9696 HB 607 CSB HA 9696 0.09 1.008
; qtot -2.778
9697 CT2 607 CSB CB 9697 -0.05 12.011
; qtot -2.828
9698 HA 607 CSB HB1 9698 0.051 1.008
; qtot -2.777
9699 HA 607 CSB HB2 9699 0.051 1.008
; qtot -2.726
9700 S 607 CSB SG 9700 -0.57 32.06
; qtot -3.296
9701 C 607 CSB C 9701 0.51 12.011
; qtot -2.786
9702 O 607 CSB O 9702 -0.51 15.999
; qtot -3.296
; residue 610 CSA rtp CSA q -0.3
9732 NH1 610 CSA N 9732 -0.47 14.007
; qtot -3.766
9733 H 610 CSA HN 9733 0.31 1.008
; qtot -3.456
9734 CT1 610 CSA CA 9734 0.07 12.011
; qtot -3.386
9735 HB 610 CSA HA 9735 0.09 1.008
; qtot -3.296
9736 CT2 610 CSA CB 9736 -0.03 12.011
; qtot -3.326
9737 HA 610 CSA HB1 9737 0.08 1.008
; qtot -3.246
9738 HA 610 CSA HB2 9738 0.08 1.008
; qtot -3.166
9739 S 610 CSA SG 9739 -0.39 32.06
; qtot -3.556
9740 C 610 CSA C 9740 0.51 12.011
; qtot -3.046
9741 O 610 CSA O 9741 -0.51 15.999
; qtot -3.556
; residue 615 NI rtp NI q +0.4
9786 NI 615 NI NI 9786 0.4 58.6934
; qtot -3.926
; residue 616 CN rtp CN q -0.5
9787 C 616 CN C1 9787 0.11 12.011
; qtot -3.816
9788 N 616 CN N1 9788 -0.61 14.007
; qtot -4.426
; residue 617 CN rtp CN q -0.5
9789 C 617 CN C1 9789 0.11 12.011
; qtot -4.316
9790 N 617 CN N1 9790 -0.61 14.007
; qtot -4.926
; residue 618 CO rtp CO q -0.1
9791 C 618 CO C1 9791 0.22 12.011
; qtot -4.706
9792 O 618 CO O1 9792 -0.294 15.999
; qtot -5
While this are the bonds I am referring:
1017 9786 1
1050 9786 1
9700 9786 1
9739 9786 1
1012 9786 1 *
1015 9786 1 *
1016 9786 1 *
1045 9786 1 *
1048 9786 1 *
1049 9786 1 *
9695 9786 1 *
9698 9786 1 *
9699 9786 1 *
9734 9786 1 *
9737 9786 1 *
9738 9786 1 *
9786 9787 1
9786 9789 1
9786 9791 1
The bonds with the * are what I call fake. i.e the couple 1012 9786
involves a bond between the nickel atom and an hydrogen.
This couple, as well as the other fake couples, disappears in the .tpr
file an interestingly pdb2gmx doesn't signal them.
Your atom numbering is non-unique, so this may be confusing something.
Try pdb2gmx -renumber, and/or feeding the renumbered .gro file into a
second run of pdb2gmx. Also, providing your specbond.dat would help when
seeking answers about how it works...
Mark
If the phenomena is not yet known, I can give you the data I used to
generate the .top and .tpr.
Francesco
Il giorno 21 marzo 2012 16:18, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> ha scritto:
On 22/03/2012 1:46 AM, francesco oteri wrote:
Dear gromacs user,
I noted a strange behavior in topology generation workflow.
I have a protein whose active site contains a Ni atom linked to 4
Cys.
I inserted the 4 bonds by specbonds.dat. When I run pdb2gmx, I
have inspected
the Linking messages and they fit with the expected topology, I
mean pdb2gmx
correctly detects the four bonds nickel-sulphur.
So I run grompp and the topol.tpr has been correctly generated.
Then I compared topol.top and topol.tpr bonds and I noticed that
in topol.top there a lot
of fake-bonds, i.e Ni-hydrogen, Ni-Carbonium.
Can you show an example of what you interpret as a fake bond?
Mark
I dumped topol.tpr through gmxdump, and I noticed that these
bonds are no more present
and only "right" bonds are present.
So, I am wondering why the fake bonds are inserted in topol.top
and how grompp detectes
these bonds.
Francesco
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--
Cordiali saluti, Dr.Oteri Francesco
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